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Protein

Histone H4

Gene

TGas006m08.1

Organism
Xenopus tropicalis (Western clawed frog) (Silurana tropicalis)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling (By similarity).By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi17 – 215By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

ReactomeiR-XTR-212300. PRC2 methylates histones and DNA.
R-XTR-2299718. Condensation of Prophase Chromosomes.
R-XTR-2559580. Oxidative Stress Induced Senescence.
R-XTR-2559582. Senescence-Associated Secretory Phenotype (SASP).
R-XTR-3214841. PKMTs methylate histone lysines.
R-XTR-3214842. HDMs demethylate histones.
R-XTR-3214847. HATs acetylate histones.
R-XTR-3214858. RMTs methylate histone arginines.
R-XTR-427413. NoRC negatively regulates rRNA expression.
R-XTR-5250924. B-WICH complex positively regulates rRNA expression.
R-XTR-5578749. Transcriptional regulation by small RNAs.
R-XTR-5693565. Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.
R-XTR-5693571. Nonhomologous End-Joining (NHEJ).
R-XTR-5693607. Processing of DNA double-strand break ends.
R-XTR-69473. G2/M DNA damage checkpoint.
R-XTR-73728. RNA Polymerase I Promoter Opening.
R-XTR-73777. RNA Polymerase I Chain Elongation.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H4
Gene namesi
ORF Names:TGas006m08.1
OrganismiXenopus tropicalis (Western clawed frog) (Silurana tropicalis)
Taxonomic identifieri8364 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusSilurana
Proteomesi
  • UP000008143 Componenti: Unassembled WGS sequence

Organism-specific databases

XenbaseiXB-GENE-5724689. hist1h4a.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleosome core, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedBy similarity
Chaini2 – 103102Histone H4PRO_0000307388Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserineBy similarity
Modified residuei2 – 21PhosphoserineBy similarity
Modified residuei4 – 41Asymmetric dimethylarginine; by PRMT1; alternateBy similarity
Modified residuei4 – 41Citrulline; alternateBy similarity
Modified residuei4 – 41Omega-N-methylarginine; by PRMT1; alternateBy similarity
Modified residuei4 – 41Symmetric dimethylarginine; by PRMT5 and PRMT7; alternateBy similarity
Modified residuei6 – 61N6-acetyllysineBy similarity
Modified residuei9 – 91N6-acetyllysineBy similarity
Modified residuei13 – 131N6-acetyllysineBy similarity
Modified residuei17 – 171N6-acetyllysineBy similarity
Modified residuei21 – 211N6,N6,N6-trimethyllysine; alternateBy similarity
Modified residuei21 – 211N6,N6-dimethyllysine; alternateBy similarity
Modified residuei21 – 211N6-methyllysine; alternateBy similarity
Modified residuei32 – 321N6-acetyllysineBy similarity
Modified residuei48 – 481Phosphoserine; by PAK2By similarity
Modified residuei52 – 521PhosphotyrosineBy similarity
Modified residuei60 – 601N6-acetyllysineBy similarity
Modified residuei80 – 801N6-acetyllysineBy similarity
Modified residuei89 – 891PhosphotyrosineBy similarity
Modified residuei92 – 921N6-acetyllysine; alternateBy similarity
Cross-linki92 – 92Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternateBy similarity

Post-translational modificationi

Acetylation at Lys-6 (H4K5ac), Lys-9 (H4K8ac), Lys-13 (H4K12ac) and Lys-17 (H4K16ac) occurs in coding regions of the genome but not in heterochromatin.By similarity
Citrullination at Arg-4 (H4R3ci) by PADI4 impairs methylation.By similarity
Monomethylation and asymmetric dimethylation at Arg-4 (H4R3me1 and H4R3me2a, respectively) by PRMT1 favors acetylation at Lys-9 (H4K8ac) and Lys-13 (H4K12ac). Demethylation is performed by JMJD6. Symmetric dimethylation on Arg-4 (H4R3me2s) by the PRDM1/PRMT5 complex may play a crucial role in the germ-cell lineage (By similarity).By similarity
Monomethylated, dimethylated or trimethylated at Lys-21 (H4K20me1, H4K20me2, H4K20me3). Monomethylation is performed by SET8. Trimethylation is performed by KMT5B and KMT5C and induces gene silencing (By similarity).By similarity
Phosphorylated by pak2 at Ser-48 (H4S47ph). This phosphorylation increases the association of H3.3-H4 with the histone chaperone HIRA, thus promoting nucleosome assembly of H3.3-H4 and inhibiting nucleosome assembly of H3.1-H4 (By similarity).By similarity
Ubiquitinated by the CUL4-DDB-RBX1 complex in response to ultraviolet irradiation. This may weaken the interaction between histones and DNA and facilitate DNA accessibility to repair proteins. Monoubiquitinated at Lys-92 of histone H4 (H4K91ub1) in response to DNA damage. The exact role of H4K91ub1 in DNA damage response is still unclear but it may function as a licensing signal for additional histone H4 post-translational modifications such as H4 Lys-21 methylation (H4K20me) (By similarity).By similarity
Sumoylated, which is associated with transcriptional repression.By similarity

Keywords - PTMi

Acetylation, Citrullination, Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiQ28DR4.
PRIDEiQ28DR4.

Expressioni

Gene expression databases

BgeeiQ28DR4.
ExpressionAtlasiQ28DR4. baseline.

Interactioni

Subunit structurei

The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA (By similarity).By similarity

Protein-protein interaction databases

STRINGi8364.ENSXETP00000063763.

Chemistry

BindingDBiQ28DR4.

Structurei

3D structure databases

ProteinModelPortaliQ28DR4.
SMRiQ28DR4. Positions 21-102.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the histone H4 family.Curated

Phylogenomic databases

eggNOGiKOG3467. Eukaryota.
COG2036. LUCA.
GeneTreeiENSGT00760000119019.
HOGENOMiHOG000234654.
HOVERGENiHBG051878.
InParanoidiQ28DR4.
KOiK11254.
OMAiFTFINIT.
OrthoDBiEOG77T174.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR001951. Histone_H4.
IPR019809. Histone_H4_CS.
IPR004823. TAF_TATA-bd.
[Graphical view]
PRINTSiPR00623. HISTONEH4.
SMARTiSM00417. H4. 1 hit.
SM00803. TAF. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00047. HISTONE_H4. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q28DR4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL
60 70 80 90 100
IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVYA LKRQGRTLYG

FGG
Length:103
Mass (Da):11,367
Last modified:April 4, 2006 - v1
Checksum:iA9E5DFD3F8B97598
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CR848633 mRNA. Translation: CAJ83618.1.
RefSeqiNP_001016869.1. NM_001016869.2.
XP_002933940.1. XM_002933894.3.
XP_002942338.1. XM_002942292.3.
XP_002943144.1. XM_002943098.3.
XP_002944234.1. XM_002944188.3.
XP_004917044.1. XM_004916987.2.
XP_004917053.1. XM_004916996.2.
XP_004917057.1. XM_004917000.2.
XP_004917064.1. XM_004917007.2.
XP_004919473.1. XM_004919416.2.
XP_004919478.1. XM_004919421.2.
XP_004919480.1. XM_004919423.2.
XP_004920262.1. XM_004920205.2.
XP_004920490.1. XM_004920433.2.
XP_012817504.1. XM_012962050.1.
XP_012817505.1. XM_012962051.1.
XP_012817506.1. XM_012962052.1.
XP_012821249.1. XM_012965795.1.
XP_012821250.1. XM_012965796.1.
UniGeneiStr.87083.

Genome annotation databases

EnsembliENSXETT00000001377; ENSXETP00000001377; ENSXETG00000000626.
ENSXETT00000044316; ENSXETP00000044316; ENSXETG00000020498.
ENSXETT00000054182; ENSXETP00000054182; ENSXETG00000025390.
ENSXETT00000054185; ENSXETP00000054185; ENSXETG00000025396.
ENSXETT00000054589; ENSXETP00000054589; ENSXETG00000025686.
ENSXETT00000054958; ENSXETP00000054958; ENSXETG00000025931.
ENSXETT00000055001; ENSXETP00000055001; ENSXETG00000025961.
ENSXETT00000055237; ENSXETP00000055237; ENSXETG00000026118.
ENSXETT00000055544; ENSXETP00000055544; ENSXETG00000026305.
ENSXETT00000056117; ENSXETP00000056117; ENSXETG00000026679.
ENSXETT00000056585; ENSXETP00000056585; ENSXETG00000026965.
ENSXETT00000056587; ENSXETP00000056587; ENSXETG00000026966.
ENSXETT00000056849; ENSXETP00000056849; ENSXETG00000027140.
ENSXETT00000056865; ENSXETP00000056865; ENSXETG00000027164.
ENSXETT00000056866; ENSXETP00000056866; ENSXETG00000027166.
ENSXETT00000056870; ENSXETP00000056870; ENSXETG00000027175.
ENSXETT00000056873; ENSXETP00000056873; ENSXETG00000027178.
ENSXETT00000056877; ENSXETP00000056877; ENSXETG00000027181.
ENSXETT00000056881; ENSXETP00000056881; ENSXETG00000027187.
ENSXETT00000056888; ENSXETP00000056888; ENSXETG00000027197.
ENSXETT00000056892; ENSXETP00000056892; ENSXETG00000027200.
ENSXETT00000056935; ENSXETP00000056935; ENSXETG00000027234.
ENSXETT00000057375; ENSXETP00000057375; ENSXETG00000027514.
ENSXETT00000060248; ENSXETP00000061007; ENSXETG00000033694.
ENSXETT00000060829; ENSXETP00000060763; ENSXETG00000033642.
ENSXETT00000060907; ENSXETP00000058936; ENSXETG00000030102.
ENSXETT00000061323; ENSXETP00000059551; ENSXETG00000031445.
ENSXETT00000061625; ENSXETP00000060942; ENSXETG00000029970.
ENSXETT00000061711; ENSXETP00000061355; ENSXETG00000033639.
ENSXETT00000062059; ENSXETP00000058860; ENSXETG00000031219.
ENSXETT00000062061; ENSXETP00000061001; ENSXETG00000033998.
ENSXETT00000062335; ENSXETP00000062223; ENSXETG00000031963.
ENSXETT00000062534; ENSXETP00000061494; ENSXETG00000030318.
ENSXETT00000062805; ENSXETP00000063397; ENSXETG00000033468.
ENSXETT00000063366; ENSXETP00000062199; ENSXETG00000030676.
ENSXETT00000063450; ENSXETP00000059940; ENSXETG00000032518.
ENSXETT00000063455; ENSXETP00000061040; ENSXETG00000032853.
ENSXETT00000064085; ENSXETP00000058765; ENSXETG00000031442.
ENSXETT00000064177; ENSXETP00000061885; ENSXETG00000031724.
ENSXETT00000064340; ENSXETP00000059040; ENSXETG00000030910.
ENSXETT00000064842; ENSXETP00000062392; ENSXETG00000033857.
ENSXETT00000065236; ENSXETP00000062836; ENSXETG00000031353.
ENSXETT00000065428; ENSXETP00000063763; ENSXETG00000032108.
ENSXETT00000065470; ENSXETP00000062225; ENSXETG00000033194.
ENSXETT00000065633; ENSXETP00000061740; ENSXETG00000032665.
ENSXETT00000066105; ENSXETP00000062375; ENSXETG00000032686.
ENSXETT00000066352; ENSXETP00000062175; ENSXETG00000034227.
GeneIDi100485962.
100488032.
100495184.
100495739.
100496758.
101732103.
101732638.
101732682.
101733182.
101734147.
101734426.
101734891.
101735268.
105947138.
105947139.
105947140.
105947733.
105947734.
549623.
KEGGixtr:100485962.
xtr:100488032.
xtr:100495184.
xtr:100495739.
xtr:100496758.
xtr:101732103.
xtr:101732638.
xtr:101732682.
xtr:101733182.
xtr:101734147.
xtr:101734426.
xtr:101734891.
xtr:101735268.
xtr:105947138.
xtr:105947139.
xtr:105947140.
xtr:105947733.
xtr:105947734.
xtr:549623.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CR848633 mRNA. Translation: CAJ83618.1.
RefSeqiNP_001016869.1. NM_001016869.2.
XP_002933940.1. XM_002933894.3.
XP_002942338.1. XM_002942292.3.
XP_002943144.1. XM_002943098.3.
XP_002944234.1. XM_002944188.3.
XP_004917044.1. XM_004916987.2.
XP_004917053.1. XM_004916996.2.
XP_004917057.1. XM_004917000.2.
XP_004917064.1. XM_004917007.2.
XP_004919473.1. XM_004919416.2.
XP_004919478.1. XM_004919421.2.
XP_004919480.1. XM_004919423.2.
XP_004920262.1. XM_004920205.2.
XP_004920490.1. XM_004920433.2.
XP_012817504.1. XM_012962050.1.
XP_012817505.1. XM_012962051.1.
XP_012817506.1. XM_012962052.1.
XP_012821249.1. XM_012965795.1.
XP_012821250.1. XM_012965796.1.
UniGeneiStr.87083.

3D structure databases

ProteinModelPortaliQ28DR4.
SMRiQ28DR4. Positions 21-102.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi8364.ENSXETP00000063763.

Chemistry

BindingDBiQ28DR4.

Proteomic databases

PaxDbiQ28DR4.
PRIDEiQ28DR4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSXETT00000001377; ENSXETP00000001377; ENSXETG00000000626.
ENSXETT00000044316; ENSXETP00000044316; ENSXETG00000020498.
ENSXETT00000054182; ENSXETP00000054182; ENSXETG00000025390.
ENSXETT00000054185; ENSXETP00000054185; ENSXETG00000025396.
ENSXETT00000054589; ENSXETP00000054589; ENSXETG00000025686.
ENSXETT00000054958; ENSXETP00000054958; ENSXETG00000025931.
ENSXETT00000055001; ENSXETP00000055001; ENSXETG00000025961.
ENSXETT00000055237; ENSXETP00000055237; ENSXETG00000026118.
ENSXETT00000055544; ENSXETP00000055544; ENSXETG00000026305.
ENSXETT00000056117; ENSXETP00000056117; ENSXETG00000026679.
ENSXETT00000056585; ENSXETP00000056585; ENSXETG00000026965.
ENSXETT00000056587; ENSXETP00000056587; ENSXETG00000026966.
ENSXETT00000056849; ENSXETP00000056849; ENSXETG00000027140.
ENSXETT00000056865; ENSXETP00000056865; ENSXETG00000027164.
ENSXETT00000056866; ENSXETP00000056866; ENSXETG00000027166.
ENSXETT00000056870; ENSXETP00000056870; ENSXETG00000027175.
ENSXETT00000056873; ENSXETP00000056873; ENSXETG00000027178.
ENSXETT00000056877; ENSXETP00000056877; ENSXETG00000027181.
ENSXETT00000056881; ENSXETP00000056881; ENSXETG00000027187.
ENSXETT00000056888; ENSXETP00000056888; ENSXETG00000027197.
ENSXETT00000056892; ENSXETP00000056892; ENSXETG00000027200.
ENSXETT00000056935; ENSXETP00000056935; ENSXETG00000027234.
ENSXETT00000057375; ENSXETP00000057375; ENSXETG00000027514.
ENSXETT00000060248; ENSXETP00000061007; ENSXETG00000033694.
ENSXETT00000060829; ENSXETP00000060763; ENSXETG00000033642.
ENSXETT00000060907; ENSXETP00000058936; ENSXETG00000030102.
ENSXETT00000061323; ENSXETP00000059551; ENSXETG00000031445.
ENSXETT00000061625; ENSXETP00000060942; ENSXETG00000029970.
ENSXETT00000061711; ENSXETP00000061355; ENSXETG00000033639.
ENSXETT00000062059; ENSXETP00000058860; ENSXETG00000031219.
ENSXETT00000062061; ENSXETP00000061001; ENSXETG00000033998.
ENSXETT00000062335; ENSXETP00000062223; ENSXETG00000031963.
ENSXETT00000062534; ENSXETP00000061494; ENSXETG00000030318.
ENSXETT00000062805; ENSXETP00000063397; ENSXETG00000033468.
ENSXETT00000063366; ENSXETP00000062199; ENSXETG00000030676.
ENSXETT00000063450; ENSXETP00000059940; ENSXETG00000032518.
ENSXETT00000063455; ENSXETP00000061040; ENSXETG00000032853.
ENSXETT00000064085; ENSXETP00000058765; ENSXETG00000031442.
ENSXETT00000064177; ENSXETP00000061885; ENSXETG00000031724.
ENSXETT00000064340; ENSXETP00000059040; ENSXETG00000030910.
ENSXETT00000064842; ENSXETP00000062392; ENSXETG00000033857.
ENSXETT00000065236; ENSXETP00000062836; ENSXETG00000031353.
ENSXETT00000065428; ENSXETP00000063763; ENSXETG00000032108.
ENSXETT00000065470; ENSXETP00000062225; ENSXETG00000033194.
ENSXETT00000065633; ENSXETP00000061740; ENSXETG00000032665.
ENSXETT00000066105; ENSXETP00000062375; ENSXETG00000032686.
ENSXETT00000066352; ENSXETP00000062175; ENSXETG00000034227.
GeneIDi100485962.
100488032.
100495184.
100495739.
100496758.
101732103.
101732638.
101732682.
101733182.
101734147.
101734426.
101734891.
101735268.
105947138.
105947139.
105947140.
105947733.
105947734.
549623.
KEGGixtr:100485962.
xtr:100488032.
xtr:100495184.
xtr:100495739.
xtr:100496758.
xtr:101732103.
xtr:101732638.
xtr:101732682.
xtr:101733182.
xtr:101734147.
xtr:101734426.
xtr:101734891.
xtr:101735268.
xtr:105947138.
xtr:105947139.
xtr:105947140.
xtr:105947733.
xtr:105947734.
xtr:549623.

Organism-specific databases

CTDi8359.
8364.
XenbaseiXB-GENE-5724689. hist1h4a.

Phylogenomic databases

eggNOGiKOG3467. Eukaryota.
COG2036. LUCA.
GeneTreeiENSGT00760000119019.
HOGENOMiHOG000234654.
HOVERGENiHBG051878.
InParanoidiQ28DR4.
KOiK11254.
OMAiFTFINIT.
OrthoDBiEOG77T174.

Enzyme and pathway databases

ReactomeiR-XTR-212300. PRC2 methylates histones and DNA.
R-XTR-2299718. Condensation of Prophase Chromosomes.
R-XTR-2559580. Oxidative Stress Induced Senescence.
R-XTR-2559582. Senescence-Associated Secretory Phenotype (SASP).
R-XTR-3214841. PKMTs methylate histone lysines.
R-XTR-3214842. HDMs demethylate histones.
R-XTR-3214847. HATs acetylate histones.
R-XTR-3214858. RMTs methylate histone arginines.
R-XTR-427413. NoRC negatively regulates rRNA expression.
R-XTR-5250924. B-WICH complex positively regulates rRNA expression.
R-XTR-5578749. Transcriptional regulation by small RNAs.
R-XTR-5693565. Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.
R-XTR-5693571. Nonhomologous End-Joining (NHEJ).
R-XTR-5693607. Processing of DNA double-strand break ends.
R-XTR-69473. G2/M DNA damage checkpoint.
R-XTR-73728. RNA Polymerase I Promoter Opening.
R-XTR-73777. RNA Polymerase I Chain Elongation.

Gene expression databases

BgeeiQ28DR4.
ExpressionAtlasiQ28DR4. baseline.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR001951. Histone_H4.
IPR019809. Histone_H4_CS.
IPR004823. TAF_TATA-bd.
[Graphical view]
PRINTSiPR00623. HISTONEH4.
SMARTiSM00417. H4. 1 hit.
SM00803. TAF. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00047. HISTONE_H4. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. Sanger Xenopus tropicalis EST/cDNA project
    Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Gastrula.

Entry informationi

Entry nameiH4_XENTR
AccessioniPrimary (citable) accession number: Q28DR4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 23, 2007
Last sequence update: April 4, 2006
Last modified: May 11, 2016
This is version 85 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.